Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

Phylogenetic and biogeographic history of brook lampreys (Lampetra: Petromyzontidae) in the river basins of the Adriatic Sea based on DNA barcode data

The Adriatic brook lamprey, Lampetra zanandreai Vladykov 1955, was described from northeastern Italy. Its distribution is thought to include left tributaries of the River Po and the river basins of the Adriatic Sea from the River Po to the River Isonzo/Soča in Italy, Switzerland and Slovenia. It also shows a geographically isolated distribution in the Potenza River on the Adriatic slope in Central Italy. Lampetra from the Neretva River system in Croatia and Bosnia and Herzegovina and the Morača River system in Montenegro that were previously identified as L. zanandreai were recently described as a new species Lampetra soljani Tutman, Freyhof, Dulčić, Glamuzina & Geiger 2017 based on morphological data and a genetic distance between the two species of roughly 2.5% in the DNA barcoding gene cytochrome oxidase I (COI). Since DNA barcodes for L. zanandreai are only available for one population from the upper Po River in northwestern Italy, we generated additional COI nucleotide sequence data of this species from Switzerland, northeastern and central Italy comprising near topotypic material and obtained GenBank sequences of the species from Slovenia to better assess the evolutionary history of the two brook lamprey species in the river basins of the Adriatic Sea. Our data show a low sequence divergence of <1% between L. zanandreai from Switzerland, northeastern and central Italy and Slovenia and the Balkan species L. soljani. However, members of the population previously identified as 'L. zanandreai' from northwest Italy are genetically highly divergent from those of L. zanandreai and likely belong to an undescribed species, L. sp. 'upper Po'. The presence of a unique and highly divergent brook lamprey lineage in the upper Po River suggests that L. zanandreai and Lampetra sp. 'upper Po' may have evolved in separate paleo drainages during the formation of the modern Po Valley subsequent to marine inundations in the Pliocene.

Genetic evidence on the occurrence of Channa harcourtbutleri (Annandale, 1918) in Eastern Ghats, India: first report from mainland India

Channa harcourtbutleri (Annandale) was described from Inle Lake (Southern Shan State) in Myanmar, and is currently considered as a valid species in the Channa gachua species-group. Notwithstanding several detailed studies on Channa from India in the recent, none has mentioned the occurrence of C. harcourtbutleri in the Indian mainland. In continuation to the faunal diversity exploration in Eastern Ghats, India, a few specimens in the C. gachua species-group were collected from the river Sabri sub-basin of the river Godavari basin in the East Godavari District of Andhra Pradesh which was identified as C. harcourtbutleri through DNA barcoding. This is a first report on occurrence of the species in the wild in the Eastern Ghats, India. 

Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 - 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (O_L) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.

Population genetics of the African snakehead fish Parachanna obscura along West Africa's water networks: Implications for sustainable management and conservation

An essential factor for aquatic conservation is genetic diversity or population divergence, which in natural populations reflects the interplay between geographical isolation with restricted gene flow and local evolution of populations. The long geological history of Africa may induce stronger among-population divergence and lower within-population divergence in fish populations of African watersheds. As an example, we studied population structure of the African snakehead fish Parachanna obscura. Our study aimed: (1) to develop a set of highly polymorphic microsatellite markers suitable for the analysis of genetic diversity among P. obscura and (2) to study the genetic diversity and structure of P. obscura populations from the West Africa region and mostly from Côte d'Ivoire, with respect to the effects of climate region and geographical distance on the genetic differentiation. A total of 259 specimens from 15 locations of P. obscura were collected over the West Africa region reflecting a high variability of pairwise geographical distances and variability of hydrological connectivity of the area. We developed a set of 21 polymorphic microsatellite markers for studying population genetics of the fish. The results showed relatively low intragenetic diversity for all the 15 locations, certainly attributable to confinement of fish in segregated catchments, resulting in limited gene flow. We also found evidence for local adaptation processes, suggested by five out of 21 microsatellite loci being under putative selection, according to BAYESCAN analysis. In turn, there was strong genetic differentiation (F _ST > 0.5) among fish from most locations, reflecting the allopatric development in watersheds without hydraulic connectivity. Neighbor-joining dendrogram, Principal Coordinate Analysis, and analysis of ancestral groups by STRUCTURE suggested that the 15 locations can be divided into three clusters, mainly matching the dominant climate zones and the segregation of the watersheds in the region. The distinct genetic structure of the fish from the 15 locations obtained in this study suggests that conservation and sustainable management actions of this fish resource should avoid genetic mixing of potentially locally adapted populations.

Chromosome complements of Channalucius and C.striata from Phu Quoc Island and karyotypic evolution in snakehead fishes (Actinopterygii, Channidae)

Snakehead fishes of the family Channidae are obligatory air-breathers freshwater predators, the vast majority of which belong to the genus Channa Scopoli, 1777. Channa species are characterized by high karyotypic diversity due to various types of chromosomal rearrangements. It is assumed that, in addition to the lifestyle, fragmentation and isolation of snakehead populations contribute to an increase in karyotypic diversity. However, the chromosome complements of many isolated populations of widespread Channa species remain unknown, and the direction of karyotype transformations is poorly understood. This paper describes the previously unstudied karyotypes of Channalucius (Cuvier, 1831) and C.striata (Bloch, 1793) from Phu Quoc Island and analyzes the trends of karyotypic evolution in the genus Channa. In C.lucius, the karyotypes are differed in the number of chromosome arms (2n = 48, NF = 50 and 51), while in C.striata, the karyotypes are differed in the diploid chromosome number (2n = 44 and 43, NF = 48). A comparative cytogenetic analysis showed that the main trend of karyotypic evolution of Channa species is associated with a decrease in the number of chromosomes and an increase in the number of chromosome arms, mainly due to fusions and pericentric inversions. The data obtained support the assumption that fragmentation and isolation of populations, especially of continental islands, contribute to the karyotypic diversification of snakeheads and are of interest for further cytogenetic studies of Channidae.

Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses

Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.

Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland

Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.

The emerging vertebrate model species for neurophysiological studies is Danionella cerebrum, new species (Teleostei: Cyprinidae)

The four described species of Danionella are tiny, transparent fishes that mature at sizes between 10–15 mm, and represent some of the most extreme cases of vertebrate progenesis known to date. The miniature adult size and larval appearance of Danionella, combined with a diverse behavioral repertoire linked to sound production by males, have established Danionella as an important model for neurophysiological studies. The external similarity between the different species of Danionella has offered an important challenge to taxonomic identification using traditional external characters, leading to confusion over the identity of the model species. Using combined morphological and molecular taxonomic approaches, we show here that the most extensively studied species of Danionella is not D. translucida, but represents an undescribed species, D. cerebrum n. sp. that is externally almost identical to D. translucida, but differs trenchantly in several internal characters. Molecular analyses confirm the distinctiveness of D. cerebrum and D. translucida and suggest that the two species are not even sister taxa. Analysis of the evolution of sexual dimorphisms associated with the Weberian apparatus reveals significant increases in complexity from the simpler condition found in D. dracula, to most complex conditions in D. cerebrum, D. mirifica and D. translucida.

Aquatic Organisms Research with DNA Barcodes

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.

Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

Impact of Pleistocene Eustatic Fluctuations on Evolutionary Dynamics in Southeast Asian Biodiversity Hotspots

Pleistocene Climatic Fluctuations (PCF) are frequently highlighted as important evolutionary engines that triggered cycles of biome expansion and contraction. While there is ample evidence of the impact of PCF on biodiversity of continental biomes, the consequences in insular systems depend on the geology of the islands and the ecology of the taxa inhabiting them. The idiosyncratic aspects of insular systems are exemplified by the islands of the Sunda Shelf in Southeast Asia (Sundaland), where PCF-induced eustatic fluctuations had complex interactions with the geology of the region, resulting in high species diversity and endemism. Emergent land in Southeast Asia varied drastically with sea level fluctuations during the Pleistocene. Climate-induced fluctuations in sea level caused temporary connections between insular and continental biodiversity hotspots in Southeast Asia. These exposed lands likely had freshwater drainage systems that extended between modern islands: the Paleoriver Hypothesis. Built upon the assumption that aquatic organisms are among the most suitable models to trace ancient river boundaries and fluctuations of landmass coverage, the present study aims to examine the evolutionary consequences of PCF on the dispersal of freshwater biodiversity in Southeast Asia. Time-calibrated phylogenies of DNA-delimited species were inferred for six species-rich freshwater fish genera in Southeast Asia (Clarias, Channa, Glyptothorax, Hemirhamphodon, Dermogenys, Nomorhamphus). The results highlight rampant cryptic diversity and the temporal localization of most speciation events during the Pleistocene, with 88% of speciation events occurring during this period. Diversification analyses indicate that sea level-dependent diversification models poorly account for species proliferation patterns for all clades excepting Channa. Ancestral area estimations point to Borneo as the most likely origin for most lineages, with two waves of dispersal to Sumatra and Java during the last 5 Myr. Speciation events are more frequently associated with boundaries of the paleoriver watersheds, with 60%, than islands boundaries, with 40%. In total, one-third of speciation events are inferred to have occured within paleorivers on a single island, suggesting that habitat heterogeneity and factors other than allopatry between islands substantially affected diversification of Sundaland fishes. Our results suggest that species proliferation in Sundaland is not wholly reliant on Pleistocene sea-level fluctuations isolating populations on different islands.

Cryptic species diversity and molecular diagnosis of Channa orientalis; an endemic freshwater fish of Sri Lanka

Fish genetic resources and diversity are very important aspects of environmental management and fisheries and are vital for making decisions on their commercial exploitation as well as conservation. The snakehead fishes in the world have significant economic importance as food and ornamental fish. A clear understanding of species' taxonomic status and genetic diversity is important for the utilization and implementation of conservation and management practices. Channa orientalis is a snakehead endemic to Sri Lanka that is heavily utilized in the ornamental fish export trade. Its genetic diversity has not yet been fully understood and it is difficult to distinguish it from closely resembling species. Therefore, we examined the genetic diversity of C. orientalis and developed a DNA-based marker that permits accurate, low cost, and reliable identification of C. orientalis. Determination of genetic diversity was mainly carried out through genetic analysis of the mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) gene. The development of the DNA-based marker for the identification of C. orientalis was done through Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. Our analyses confirmed the presence of two distinct genetically divergent and geographically separated lineages of C. orientalis in Sri Lanka. The fast cost-effective gel-based PCR-RFLP marker method developed by us was successful in diagnosing C. orientalis from its closely resembling species. Thus, we believe our findings on the cryptic diversity and diagnostic methods will have important implications for the conservation and management of this endemic species.

Aenigmachannidae, a new family of snakehead fishes (Teleostei: Channoidei) from subterranean waters of South India

Pronounced organism-wide morphological stasis in evolution has resulted in taxa with unusually high numbers of primitive characters. These ‘living fossils’ hold a prominent role for our understanding of the diversification of the group in question. Here we provide the first detailed osteological analysis of Aenigmachanna gollum based on high-resolution nano-CT scans and one cleared and stained specimen of this recently described snakehead fish from subterranean waters of Kerala in South India. In addition to a number of derived and unique features, Aenigmachanna has several characters that exhibit putatively primitive conditions not encountered in the family Channidae. Our morphological analysis provides evidence for the phylogenetic position of Aenigmachanna as the sister group to Channidae. Molecular analyses further emphasize the uniqueness of Aenigmachanna and indicate that it is a separate lineage of snakeheads, estimated to have split from its sister group at least 34 or 109 million years ago depending on the fossil calibration employed. This may indicate that Aenigmachanna is a Gondwanan lineage, which has survived break-up of the supercontinent, with India separating from Africa at around 120 mya. The surprising morphological disparity of Aenigmachanna from members of the Channidae lead us to erect a new family of snakehead fishes, Aenigmachannidae, sister group to Channidae, to accommodate these unique snakehead fishes.

DNA Barcoding Silver Butter Catfish (Schilbe intermedius) Reveals Patterns of Mitochondrial Genetic Diversity Across African River Systems

The silver butter catfish (Schilbe intermedius) is widely distributed across African river systems. To date, information on its mitochondrial genetic diversity, population structure, and historical demography are not well-established. Herein, we combined newly generated mitochondrial cytochrome c oxidase (COI) subunit I gene sequences with previously published COI sequences in the global databases to reconstruct its phylogeography, population genetic structure, and historical demography. Results from the mtDNA phylogeography and species delimitation tests (Cluster algorithm - Species Identifier, Automatic Barcode Gap Discovery and Poison Tree Process model) revealed that S. intermedius comprises at least seven geographically defined matrilines. Although the overall haplotype diversity of S. intermedius was high (h = 0.90), results showed that East (Kenya) and West (Nigeria) African populations had low levels of haplotype diversity (h = ~0.40). In addition, population genetic polymorphism and historical demographics showed that S. intermedius populations in both East and West Africa underwent severe contractions as a result of biogeographic influences. The patterns of genetic diversity and population structure were consistent with adaptive responses to historical biogeographic factors and contemporary environmental variations across African river systems. This is suggestive of the influence of historical biogeographic factors and climatic conditions on population divergence of S. intermedius across African river systems. Given our discovery of previously underappreciated diversity within S. intermedius, we recommend that this species be considered for increased conservation and management.

Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

DNA barcoding of freshwater fishes from Brahmaputra River in Eastern Himalaya biodiversity hotspot

The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36–10.73%) was detected in 11 species (Macrognathus pancalus, Channa punctata, Puntius terio, Bangana ariza, Garra arupi, Badis badis, Mystus vittatus, Rita rita, Gagata cenia, Mastacembelus armatus, and Danio dangila), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species: Channa stiktos and C. ornatipinnis (1.43%); Mystus ngasep, M. rufescens, and M. carcio (0.4%); Glyptothorax trilineatus, G. churamanii, and G. verrucosus (0.4%); Botia almorhae, B. histrionica, B. lohachata, and B. rostrata (0–0.4%); Barilius barilia and B. vagra (0.4%); Batasio merianiensis and B. tengana (1.2%); Puntius chola and P. fraseri (0%), Schistura beavani and S. paucireticulata (0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.

Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Background: Kelabau (Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 (CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%–97% in GenBank and 96.6%–96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

Biometric and genetic differences in kelabau ( Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Background: Kelabau ( Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 ( CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%-97% in GenBank and 96.6%-96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

Biometric and genetic differences in kelabau ( Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1

Background: Kelabau ( Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 ( CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%-97% in GenBank and 96.6%-96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

Undocumented translocations spawn taxonomic inflation in Sri Lankan fire rasboras (Actinopterygii, Cyprinidae)

A recent (2013) taxonomic review of the freshwater-fish genus Rasboroides, which is endemic to Sri Lanka, showed it to comprise four species: R. vaterifloris, R. nigromarginatus, R. pallidus and R. rohani. Here, using an integrative-taxonomic analysis of morphometry, meristics and mitochondrial DNA sequences of cytochrome b (cytb) and cytochrome oxidase subunit 1 (coi), we show that R. nigromarginatus is a synonym of R. vaterifloris, and that R. rohani is a synonym of R. pallidus. The creation and recognition of unnecessary taxa (‘taxonomic inflation’) was in this case a result of selective sampling confounded by a disregard of allometry. The population referred to R. rohani in the Walawe river basin represents an undocumented trans-basin translocation of R. pallidus, and a translocation into the Mahaweli river of R. vaterifloris, documented to have occurred ca 1980, in fact involves R. pallidus. A shared haplotype suggests the latter introduction was likely made from the Bentara river basin and not from the Kelani, as claimed. To stabilize the taxonomy of these fishes, the two valid species, R. vaterifloris and R. pallidus, are diagnosed and redescribed, and their distributions delineated. We draw attention to the wasteful diversion of conservation resources to populations resulting from undocumented translocations and to taxa resulting from taxonomic inflation. We argue against translocations except where mandated by a conservation emergency, and even then, only when supported by accurate documentation.

Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae)

The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.